NACDDB - The Web Server for DNA,RNA,and Hybrids Circular Dichroism Structure

Hybridization of the bridged oligonucleotides with DNA: thermodynamic and kinetic studies

Overview of Pyshnyi DV et al.

AuthorsPyshnyi DV  Lomzov AA  Pyshnaya IA  Ivanova EM  
AffiliationInstitute of Chemical Biology and Fundamental Medicine   Siberian Branch of the Russian Academy of Sciences   Prospect Akad. Lavrentyeva 8   630090   Novosibirsk   Russia. pyshnyi@niboch.nsc.ru  
JournalJ Biomol Struct Dyn
Year 2006

Abstract


Hybridization properties of oligonucleotides containing non-nucleotide inserts designed on the basis of synthetic abasic sites, oligomethylene diols or oligoethylene glycols have been characterized. The influence of the inserts which generate extrahelical anucleotidic bulges on thermodynamics, kinetics of hybridization of bridged oligonucleotide with DNA has been studied by UV-melting and stopped-flow techniques. Circular dichroism spectrometry data show that anucleotidic bulges in the middle of the duplex does not alter the B-form helix conformation. Nevertheless, the insert induces destabilization of the duplex structure, caused mostly by the considerable enhancement of the dissociation rates. Free energy increments for the extrahelical anucleotidic bulges can be described in the nearest-neighbor approximation. The thermodynamic effect of the insert lengthening obeys a simple Jacobson-Stockmayer entropy extrapolation. Independently of the insert type, the free energy term is directly proportional to the logarithm of the number of bonds between the oligonucleotide fragments. The behavior of hydrophobic inserts formed by 10-hydroxydecyl-1-phospate units is an exception to the rule.